Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes

Coon, Kerri L.; Hegde, Shivanand; Hughes, Grant L

doi:10.1101/2021.10.06.463328

Cited by 2 publications

(1 citation statement)

References 89 publications

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“…The data retrieved in this study agrees with published insights; the phylum level classifications are consistent with findings from other mosquito microbiome studies (8,9,11,18,72,73), showing that Proteobacteria, Bacteroidetes and Firmicutes are dominant phyla of the mosquito microbiome; and our taxonomic classifications highlight the inherent variability of the Aedes aegypti microbiome (18,24,74). These findings give us confidence that taxonomic classifications with KRAKEN2, within the pipeline, can accurately predict the presence of microbes associated to the Aedes aegypti microbiome from non-reference sequences.…”

Section: Discussionsupporting

confidence: 92%

Recovery of Metagenomic Data from theAedes aegyptiMicrobiome using a Reproducible Snakemake Pipeline: MINUUR

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Cerdeira

Hughes

et al. 2022

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The microbiome is a collection of microbes that exist in symbiosis with a host. Whole genome sequencing produces off-target, non-specific reads, to the host in question, which can be used for metagenomic inference of a microbiome. This data is advantageous over barcoding methods since higher taxonomic resolution and functional predictions of microbes are possible. With the growing number of genomic sequencing data publicly available, comes opportunity to elucidate reads pertaining to the microbiome. However, characterization of these reads can be complex, with many steps required to perform a robust analysis. To address this, we developed MINUUR (Microbial INsights Using Unmapped Reads); a snakemake pipeline to characterize non-host reads from existing genomic data. We apply this pipeline to ten, publicly available, high coverage Aedes aegypti (Ae. aegypti) genomic samples. Using MINUUR, we describe species level microbial classifications; predict microbe associated genes and pathways and find bacterial metagenome assembled genomes (MAGs) associated to the Ae. aegypti microbiome. Of these MAGS, 19 are high-quality representatives with over 90% completeness and under 5% contamination. In summary, we present an in-depth analysis of non-host reads from Ae. aegypti whole genome sequencing data within a reproducible and open-access pipeline.

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Section: Discussionsupporting

confidence: 92%

Recovery of Metagenomic Data from theAedes aegyptiMicrobiome using a Reproducible Snakemake Pipeline: MINUUR

Foo

Cerdeira

Hughes

et al. 2022

Preprint

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Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Foo,

Brettell,

Nichols

et al. 2023

Preprint

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Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such asPlasmodiumspp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterialMosquito-Associated IsolateCollection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of theEnterobacteriaceaecomprising 40% of the collection. Phylogenomic analysis of three genera,Enterobacter, Serratia, andElizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species’ pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to identify functions underlying mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource to investigate factors for bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.

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Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes

Cited by 2 publications

References 89 publications

Recovery of Metagenomic Data from theAedes aegyptiMicrobiome using a Reproducible Snakemake Pipeline: MINUUR

Recovery of Metagenomic Data from theAedes aegyptiMicrobiome using a Reproducible Snakemake Pipeline: MINUUR

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

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